RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5pl0gd/RM_125264.SunJan10956382023 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1672595797 Database = /dev/shm/rModeler.5pl0gd/GCF_017639515.1_sCarCar2.pri - Sequences = 719 - Bases = 4286311191 - N50 = 171616123 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 255834147-274107945 | [ 1 ] 237560350-255834147 | [ 1 ] 219286553-237560350 | [ 1 ] 201012756-219286553 | [ 2 ] 182738959-201012756 | [ 2 ] 164465162-182738959 | [ 4 ] 146191365-164465162 | [ 3 ] 127917568-146191365 | [ 1 ] 109643771-127917568 | [ 5 ] 91369974-109643771 | [ ] 73096177-91369974 | [ 1 ] 54822380-73096177 | [ 1 ] 36548583-54822380 | [ 5 ] 18274786-36548583 | [ 7 ] 989-18274786 |************************************************** [ 685 ] Storage Throughput = excellent ( 1108.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40313722 bp ( 40032745 non ambiguous ) - Num Contigs Represented = 69 - Sequence extraction : 00:04:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:20 (hh:mm:ss) Elapsed Time Round Time: 00:40:54 (hh:mm:ss) Elapsed Time : 477 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15094 repeats masked totaling 4572253 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10122712 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10011039 bp After Masking: 3397186 bp Masked: 66.07 % -- Input Database Coverage: 10122712 bp out of 4286311191 bp ( 0.24 % ) Sampling Time: 00:11:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:04:12 (hh:mm:ss) Elapsed Time, 5801 HSPs Collected Number of families returned by RECON: 788 Round Time: 00:16:13 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44283 repeats masked totaling 13786972 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30190930 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30021626 bp After Masking: 9751330 bp Masked: 67.52 % -- Input Database Coverage: 40313642 bp out of 4286311191 bp ( 0.94 % ) Sampling Time: 00:38:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:17:19 (hh:mm:ss) Elapsed Time, 36814 HSPs Collected Number of families returned by RECON: 2334 Round Time: 00:56:59 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:43:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140420 repeats masked totaling 43860077 bp(s). - TE Masking time 00:01:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90438957 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 90018811 bp After Masking: 26848157 bp Masked: 70.17 % -- Input Database Coverage: 130752599 bp out of 4286311191 bp ( 3.05 % ) Sampling Time: 01:55:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 01:45:47 (hh:mm:ss) Elapsed Time, 138722 HSPs Collected Number of families returned by RECON: 6093 Round Time: 04:00:38 (hh:mm:ss) Elapsed Time : 267 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 05:37:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 459948 repeats masked totaling 140575630 bp(s). - TE Masking time 00:07:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271137419 bp Num Contigs Represented = 239 Non ambiguous bp: Initial: 270003620 bp After Masking: 72202614 bp Masked: 73.26 % -- Input Database Coverage: 401890018 bp out of 4286311191 bp ( 9.38 % ) Sampling Time: 06:07:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 09:50:24 (hh:mm:ss) Elapsed Time, 307175 HSPs Collected Number of families returned by RECON: 17001 Round Time: 16:10:04 (hh:mm:ss) Elapsed Time : 585 families discovered. RepeatScout/RECON discovery complete: 1427 families found Classification Time: 00:51:42 (hh:mm:ss) Elapsed Time Program Time: 22:56:30 (hh:mm:ss) Elapsed Time